[phenixbb] refinement for ligands with alternative conformation

zhengyi at msu.edu zhengyi at msu.edu
Mon Mar 21 06:35:32 PDT 2011


I am working on the refinement of a structure about 2.8A, which the substrate ligand has an odd conformation. A blob of negative difference density about 4.8 sigma between the one portion of the ligand and the other. If I break down the ligand into two parts, the negative density disappears, however, one part of the ligands does not fit well. We suspect a mixture of conformations.

Any suggestions would be appreciated on how to setup refinement for ligands with alternative conformation.

Many thanks,

Yi Zheng
Department of Biochemistry
Michigan State University
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